Preparing for a no-deal Brexit forced the Northern Ireland government to “cannibalise” departments, a senior civil servant has said.

Speaking during the Covid-19 inquiry on Thursday, Denis McMahon, permanent secretary for the Northern Irish executive, explained how the unique political impact of Brexit to Northern Ireland – which shares a land border with the EU – took up large amounts of civil service focus and diverted it from emergency planning.

“We had to cannibalise departments in order to move people out of areas of work and into preparations for an EU exit,” McMahon told the inquiry.

Talking about the decision to leave the EU, McMahon said: “We had a situation where we have this uniquely contentious political situation to deal with without ministers.

“Unlike other parts of the UK we were getting we were preparing for the potential impacts of new border arrangements.”

Talking about whether Northern Ireland was prepared for a pandemic, McMahon stressed that this wasn’t “an excuse”, but that the context was necessary to explain the “effects on administration”.

“We were genuinely scared of the consequences of a no-deal exit,” he said.

This redistribution of resources also compounded a staffing issue, where Northern Ireland saw a large drop in the number of civil servants it employed.

But McMahon also argued that Operation Yellowhammer – a cross-government plan to prepare for a no-deal Brexit – had benefits for pandemic planning.

“Whatever the view of the inquiry is as to how we performed, it would have been immeasurably worse [without Operation Yellowhammer],” he said.

Other civil servants and politicians have mentioned the effect that preparations for a no-deal Brexit had on emergency planning during the first module of the official Covid-19 inquiry.

Katharine Hammond, the former director of the civil contingencies secretariat in the Cabinet Office, said Operation Yellowhammer was “a really major consumer of resources in [her] time”.

Deputy prime minister Oliver Downden defended preparations for a no-deal Brexit, telling the inquiry: “It is worth remembering the kinds of frankly apocryphal warnings that were being delivered about the consequences of no-deal Brexit, for example, in relation to medical supplies,” and adding: “It was appropriate that we shifted the resilience function to deal with this.”

The inquiry today also heard McMahon acknowledge that emergency planning documents in Northern Ireland were woefully out of date and barely mentioned pandemic risk. The majority had not been updated since 2016, with one dating back to March 2002.

The inquiry continues.